How can I put a modifier at the top of the modifier stack?
Suppose you have two modifiers like this:



Note that the second modifier is named "Subsurf".  You can move it up like this:

bpy.ops.object.modifier_move_up(modifier="Subsurf")


You may need to set the active object first, as described in this answer:

my_object = bpy.context.scene.objects['Cube']
bpy.context.scene.objects.active = my_object


If your modifier is in an unknown position in the stack, you can use a loop like this to bring it to the top:

while my_object.modifiers[0].name != "Subsurf":
    bpy.ops.object.modifier_move_up(modifier="Subsurf")